Physical Sciences and Mathematics Commons^™

Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield

Theses and Dissertations

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing …

Average Mass Scan Of The Total Ion Chromatogram Versus Percentage Chemical Composition In Multivariate Statistical Comparison Of Complex Volatile Mixtures, Niko Radulovic, Polina Blagojevic, Danielle Skropeta

Danielle Skropeta

The analysis of complex volatile mixtures by gas chromatography-mass spectrometry (GC-MS) is a time-consuming process. It involves separation and identification of the components based on their retention times and fragmentation patterns, followed by determination of their relative percentages from integration of their peak areas. Herein we show that multivariate statistical analysis of the relative abundances of the m/z values obtained from the average mass scans (AMS) of the complex mixture is a faster and potentially more reliable method of assessing these mixtures. To achieve this, 15 model complex mixtures, were prepared comprising varying amounts of 10 different constituents. The AMS …

Optically Stimulated Luminescence Dating Of Single And Multiple Grains Of Quartz From Perennially Frozen Loess In Western Yukon Territory, Canada: Comparison With Radiocarbon Chronologies For The Late Pleistocene Dawson Tephra, Richard Roberts, Lee Arnold, Martina Demuro, F Brock, D Froese, C Bronk Ramsey

Richard G Roberts

No abstract provided.

Comparative Study Of Biological And Artificial Neural Networks, O S. Eluyode, Dr. Dipo Theophilus Akomolafe Mbcs, Mncs, Mcpn,

Dr. Dipo Theophilus Akomolafe MBCS, MNCS, MCPN,

In this research project, the features of biological and artificial neural networks were studied by reviewing the existing works of authorities in print and electronics on biological and artificial neural networks. The features were then assessed and evaluated and comparative analysis of the two networks was carried out. The metrics such as structures, layers, size and functional capabilities of neurons, learning capabilities, style of computation, processing elements, processing speed, connections, strength, information storage, information transmission, communication media selection, signal transduction and fault tolerance were used as basis for comparison. A major finding in the research showed that artificial neural networks …

Process-Evaluation Of Tropospheric Humidity Simulated By General Circulation Models Using Water Vapor Isotopologues: 1. Comparison Between Models And Observations, Camille Risi, David Noone, John Worden, Christian Frankenberg, Gabriele Stiller, Michael Kiefer, Bernd Funke, Kaley Walker, Peter Bernath, Matthias Schneider, Debra Wunch, Vanessa Sherlock, Nicholas M. Deutscher, David W. Griffith, Paul O. Wennberg, Kimberly Strong, Dan Smale, Emmanuel Mahieu, Sabine Barthlott, Frank Hase, Omar Garcia, Justus Notholt, Thorsten Warneke, Geoffrey Toon, David Sayres, Sandrine Bony, Jeonghoon Lee, Derek Brown, Ryu Uemura, Christophe Sturm

Faculty of Science - Papers (Archive)

[1] The goal of this study is to determine how H2O and HDO measurements in water vapor can be used to detect and diagnose biases in the representation of processes controlling tropospheric humidity in atmospheric general circulation models (GCMs). We analyze a large number of isotopic data sets (four satellite, sixteen ground-based remote-sensing, five surface in situ and three aircraft data sets) that are sensitive to different altitudes throughout the free troposphere. Despite significant differences between data sets, we identify some observed HDO/H2O characteristics that are robust across data sets and that can be used to evaluate models. We evaluate …

Atmospheric Greenhouse Gases Retrieved From Sciamachy: Comparison To Ground-Based Fts Measurements And Model Results, O Schneising, P Bergamaschi, H Bovensmann, M Buchwitz, J P. Burrows, N M. Deutscher, D W. T Griffith, J Heymann, R Macatangay, J Messerschmidt, J Notholt, M Rettinger, M Reuter, R Sussmann, Voltaire A. Velazco, T Warneke, P O. Wennberg, D Wunch

Faculty of Science - Papers (Archive)

SCIAMACHY onboard ENVISAT (launched in 2002) enables the retrieval of global long-term columnaveraged dry air mole fractions of the two most important anthropogenic greenhouse gases carbon dioxide and methane (denoted XCO₂ and XCH₄). In order to assess the quality of the greenhouse gas data obtained with the recently introduced v2 of the scientific retrieval algorithm WFM-DOAS, we present validations with ground-based Fourier Transform Spectrometer (FTS) measurements and comparisons with model results at eight Total Carbon Column Observing Network (TCCON) sites providing realistic error estimates of the satellite data. Such validation is a prerequisite to assess the suitability …

Australia's Black Saturday Fires - Comparison Of Techniques For Estimating Emissions From Vegetation Fires, Clare Paton-Walsh, Louisa K. Emmons, Christine Wiedinmyer

Faculty of Science - Papers (Archive)

We present a comparison of techniques for estimating atmospheric emissions from fires using Australia's 2009 "Black Saturday" wildfires as a case study. Most of the fires started on Saturday the 7th of February 2009 (a date now known as "Black Saturday") and then spread rapidly, fanned by gale force winds, creating several firestorms and killing 173 people. The fires continued into early March, when rain and cooler conditions allowed the fires to be extinguished. In this study, we compare two new techniques (and one more established method) to estimate the total emissions of a number of atmospheric trace gases from …

Methane Retrievals From Greenhouse Gases Observing Satellite (Gosat) Shortwave Infrared Measurements: Performance Comparison Of Proxy And Physics Retrieval Algorithms, D Schepers, S Guerlet, A Butz, J Landgraf, C Frankenberg, O Hasekamp, J-F Blavier, N M. Deutscher, D W. T Griffith, F Hase, E Kyro, I Morino, V Sherlock, R Sussmann, I Aben

Faculty of Science - Papers (Archive)

We compare two conceptually different methods for determining methane column-averaged mixing ratios (X_CH4) from Greenhouse Gases Observing Satellite (GOSAT) shortwave infrared (SWIR) measurements. These methods account differently for light scattering by aerosol and cirrus. The proxy method retrieves a CO₂ column which, in conjunction with prior knowledge on CO₂ acts as a proxy for scattering effects. The physics-based method accounts for scattering by retrieving three effective parameters of a scattering layer. Both retrievals are validated on a 19-month data set using ground-based X_CH4 measurements at 12 stations of the Total Carbon Column Observing Network (TCCON), …

A Comparison Of Bushfire Fuel Hazard Assessors And Assessment Methods In Dry Sclerophyll Forest Near Sydney, Australia, Penny J. Watson, Sandra H. Penman, Ross A. Bradstock

Faculty of Science - Papers (Archive)

Over the last decade, fire managers in Australia have embraced the concept of ‘fuel hazard’, and guides for its assessment have been produced. The reliability of these new metrics, however, remains to be determined. This study compared fuel hazard ratings generated by five assessment teams using two Australian hazard assessment methods, in two dry sclerophyll forest sites on Sydney’s urban fringe. Attributes that underpin hazard scores, such as cover and height of various fuel layers, were also assessed. We found significant differences between teams on most variables, including hazard scores. These differences were more apparent when fuel hazard assessments focussed …

Atmospheric Carbon Dioxide Retrieved From The Greenhouse Gases Observing Satellite (Gosat): Comparison With Ground-Based Tccon Observations And Geos-Chem Model Calculations, A Cogan, H Boesch, R Parker, L Feng, Paul Palmer, J-F Blavier, Nicholas M. Deutscher, Ronald Macatangay, Justus Notholt, C M. Roehl, Thorsten Warneke, Debra Wunch

Faculty of Science - Papers (Archive)

We retrieved column-averaged dry air mole fractions of atmospheric carbon dioxide (XCO 2) from backscattered short-wave infrared (SWIR) sunlight measured by the Japanese Greenhouse gases Observing SATellite (GOSAT). Over two years of XCO 2 retrieved from GOSAT is compared with XCO 2 inferred from collocated SWIR measurements by seven ground-based Total Carbon Column Observing Network (TCCON) stations. The average difference between GOSAT and TCCON XCO 2 for individual TCCON sites ranges from -0.87 ppm to 0.77 ppm with a mean value of 0.1 ppm and standard deviation of 0.56 ppm. We find an average bias between all GOSAT and TCCON …

Comparison Of Chemical Constituents And Antibacterial Activities And Antioxidant Activities Of The Essential Oil From Leaves And Fruits Of Bridelia Retusa (L.) A. Juss, D Sanseera, W Niwatananun, Saisunee Liawruangrath, Apiwat Baramee, Banyong Khantawa, Stephen G. Pyne, Boonsom Liawruangrath

Faculty of Science - Papers (Archive)

The essential oils from the leaves and fruits of Bridelia retusa (L.) A.Juss. were isolated by hydrodistillation. The essential oils were obtained in 0.0013% yield as a pale yellow liquid and 0.0026% yield as a violet-light brown liquid for the leaf oil and fruit oil respectively. The composition of each essential oil was analysed by means of GC-(FID) and GC-MS. Eleven constituents accounting for 48.77% of total leaves oil were identified. The most abundant compound was phytol (33.4%), followed by phthalic acid (5.2%), 6, 13-dimethoxy-2, 3, 9, 10-tetramethylpentacene-1, 4, 8, 11-tetrone (3.4%), heptacosane (2.3%) and nonacosane (1.2%). Sixteen constituents accounting …

A Comparison Of Spatially Explicit And Classic Regression Modelling Of Live Coral Cover Using Hyperspectral Remote-Sensing Data In The Al Wajh Lagoon, Red Sea, S Hamylton

Faculty of Science - Papers (Archive)

Live coral is a key component of the Al Wajh marine reserve in the Red Sea. The management of this reserve is dependent on a sound understanding of the existing spatial distribution of live coral cover and the environmental factors influencing live coral at the landscape scale. This study uses remote-sensing techniques to develop ordinary least squares and spatially lagged autoregressive explanatory models of the distribution of live coral cover inside the Al Wajh lagoon, Saudi Arabia. Live coral was modelled as a response to environmental controls such as water depth, the concentration of suspended sediment in the water column …

The Long Life Of Birds: The Rat-Pigeon Comparison Revisited, William A. Buttemer, Anthony J. Hulbert, M K. Montgomery

Faculty of Science - Papers (Archive)

The most studied comparison of aging and maximum lifespan potential (MLSP) among endotherms involves the 7-fold longevity difference between rats (MLSP 5y) and pigeons (MLSP 35y). A widely accepted theory explaining MLSP differences between species is the oxidative stress theory, which purports that reactive oxygen species (ROS) produced during mitochondrial respiration damage bio-molecules and eventually lead to the breakdown of regulatory systems and consequent death. Previous rat-pigeon studies compared only aspects of the oxidative stress theory and most concluded that the lower mitochondrial superoxide production of pigeons compared to rats was responsible for their much greater longevity. This conclusion is …

Methane Observations From The Greenhouse Gases Observing Satellite: Comparison To Ground-Based Tccon Data And Model Calculations, Robert Parker, Hartmut Boesch, Austin Cogan, Annemarie Fraser, Liang Feng, Paul Palmer, Janina Messerschmidt, Nicholas M. Deutscher, David W. Griffith, Justus Notholt, Paul O. Wennberg, Debra Wunch

Faculty of Science - Papers (Archive)

We report new short-wave infrared (SWIR) column retrievals of atmospheric methane (X CH4) from the Japanese Greenhouse Gases Observing SATellite (GOSAT) and compare observed spatial and temporal variations with correlative ground-based measurements from the Total Carbon Column Observing Network (TCCON) and with the global 3-D GEOS-Chem chemistry transport model. GOSAT X CH4 retrievals are compared with daily TCCON observations at six sites between April 2009 and July 2010 (Bialystok, Park Falls, Lamont, Orleans, Darwin and Wollongong). GOSAT reproduces the site-dependent seasonal cycles as observed by TCCON with correlations typically between 0.5 and 0.7 with an estimated single-sounding precision between 0.4-0.8%. …

Comparison Of Wetland Assessment Methods, Kerstin Green

HCNSO Student Theses and Dissertations

After many decades of being considered useless and often destroyed wetlands have become valued for the many functions they provide. To make informed wetland management decisions biologists have to develop practical, rapid, and inexpensive ways to assess biological conditions and functions. Ideally these assessment methods have to measure more than one attribute of the wetland to represent the overall condition of the biological community. For this project I conducted field assessments at mitigation sites in Pembroke Pines, Florida, to see how the newest method used in the State of Florida, the Uniform Mitigation Assessment Method (UMAM), compared to the older …

Retrieval Of Atmospheric Co2 With Enhanced Accuracy And Precision From Sciamachy: Validation With Fts Measurements And Comparison With Model Results, M Reuter, H Bovensmann, M Buchwitz, Jp Burrows, B Connor, Nicholas M. Deutscher, David W. Griffith, J Heymann, Gretchen Keppel-Aleks, Janina Messerschmidt, Justus Notholt, Christof Petri, J Robinson, O Schneising, V Sherlock, Voltaire A. Velazco, Thorsten Warneke, Paul O. Wennberg, Debra Wunch

Faculty of Science - Papers (Archive)

The Bremen Optimal Estimation differential optical absorption spectroscopy (DOAS) (BESD) algorithm for satellite based retrievals of XCO 2 (the column-average dry-air mole fraction of atmospheric CO 2) has been applied to Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) data. It uses measurements in the O 2-A absorption band to correct for scattering of undetected clouds and aerosols. Comparisons with precise and accurate ground-based Fourier transform spectrometer (FTS) measurements at four Total Carbon Column Observing Network (TCCON) sites have been used to quantify the quality of the new SCIAMACHY XCO 2 data set. Additionally, the results have been compared to …

Average Mass Scan Of The Total Ion Chromatogram Versus Percentage Chemical Composition In Multivariate Statistical Comparison Of Complex Volatile Mixtures, Niko Radulovic, Polina Blagojevic, Danielle Skropeta

Faculty of Science - Papers (Archive)

The analysis of complex volatile mixtures by gas chromatography-mass spectrometry (GC-MS) is a time-consuming process. It involves separation and identification of the components based on their retention times and fragmentation patterns, followed by determination of their relative percentages from integration of their peak areas. Herein we show that multivariate statistical analysis of the relative abundances of the m/z values obtained from the average mass scans (AMS) of the complex mixture is a faster and potentially more reliable method of assessing these mixtures. To achieve this, 15 model complex mixtures, were prepared comprising varying amounts of 10 different constituents. The AMS …

The Soils Of Kiritimati (Christmas) Island, Kiribati, Central Pacific: New Information And Comparison With Previous Studies, Colin D. Woodroffe, Robert John Morrison

Faculty of Science - Papers (Archive)

No abstract provided.

Uptake And Internalisation Of Copper By Three Marine Microalgae: Comparison Of Copper-Sensitive And Copper-Tolerant Species, Jacqueline L. Levy, Brad M. Angel, Jennifer L. Stauber, Wing L. Poon, Stuart L. Simpson, Shuk Han Cheng, Dianne F. Jolley

Faculty of Science - Papers (Archive)

Although it has been well established that different species of marine algae have different sensitivities to metals, our understanding of the physiological and biochemical basis for these differences is limited. This study investigated copper adsorption and internalisation in three algal species with differing sensitivities to copper. The diatom Phaeodactylum tricornutum was particularly sensitive to copper, with a 72-h IC50 (concentration of copper to inhibit growth rate by 50%) of 8.0 μg Cu L^-1, compared to the green algae Tetraselmis sp. (72-h IC50 47 μg Cu L^-1) and Dunaliella tertiolecta (72-h IC50 530 μg Cu L^{-1 …}

Global Airs And Mopitt Co Measurements: Validation, Comparison, And Links To Biomass Burning Variations And Carbon Cycle, Leonid N. Yurganov, W. Wallace Mcmillan, Anatoly V. Dzhola, Evgeny I. Grechko, Nicholas B. Jones, Guido R. Van Der Werf

Faculty of Science - Papers (Archive)

New results of CO global total column measurements using the Atmospheric Infrared Sounder (AIRS) aboard the Aqua satellite in comparison with Measurements of Pollution in the Troposphere (MOPITT) sensor aboard the Terra satellite are presented. Both data sets are validated using ground-based total column measurements in Russia and Australia. A quality parameter based on the Profile Percent A Priori values from the standard MOPITT product is introduced. AIRS data (version 4) for biomass burning events are in agreement or lower than both MOPITT and ground measurements, but CO bursts can be seen by AIRS in most cases. For the cases …

Comparison Of Mass Spectrometry And Other Techniques For Probing Interactions Between Metal Complexes And Dna, Thitima Urathamakul, Daniel J. Waller, Jennifer L. Beck, Janice Aldrich-Wright, Stephen F. Ralph

Faculty of Science - Papers (Archive)

Electrospray ionization mass spectrometry (ESI-MS) was used to study the binding interactions of two series of ruthenium complexes, [Ru(phen)2L]2+ and [RuL′2(dpqC)]2+, to a double stranded DNA hexadecamer, and derive orders of relative binding affinity. These were shown to be in good agreement with orders of relative binding affinity derived from absorption and circular dichroism (CD) spectroscopic examination of the same systems and from DNA melting curves. However, the extent of luminescence enhancement caused by the addition of DNA to solutions of the ruthenium complexes showed little correlation with orders of binding affinity derived from ESI-MS or any of the other …

Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark R. Wilson, Xi Yang Wu, Idris Barchia, Karl A Bettelheim, Steven Driesen, Darren J. Trott, Toni A. Chapman, James J C Chin

Faculty of Science - Papers (Archive)

A combination of uni- and multiplex PCR assays targeting 58 virulence genes (VGs) associated with Escherichia coli strains causing intestinal and extraintestinal disease in humans and other mammals was used to analyze the VG repertoire of 23 commensal E. coli isolates from healthy pigs and 52 clinical isolates associated with porcine neonatal diarrhea (ND) and postweaning diarrhea (PWD). The relationship between the presence and absence of VGs was interrogated using three statistical methods. According to the generalized linear model, 17 of 58 VGs were found to be significant (P < 0.05) in distinguishing between commensal and clinical isolates. Nine of the 17 genes represented by iha, hlyA, aidA, east1, aah, fimH, iroN(E. coli), traT, and saa have not been previously identified as important VGs in clinical porcine isolates in Australia. The remaining eight VGs code for fimbriae (F4, F5, F18, and F41) and toxins (STa, STb, LT, and Stx2), normally associated with porcine enterotoxigenic E. coli. Agglomerative hierarchical algorithm analysis grouped E. coli strains into subclusters based primarily on their serogroup. Multivariate analyses of clonal relationships based on the 17 VGs were collapsed into two-dimensional space by principal coordinate analysis. PWD clones were distributed in two quadrants, separated from ND and commensal clones, which tended to cluster within one quadrant. Clonal subclusters within quadrants were highly correlated with serogroups. These methods of analysis provide different perspectives in our attempts to understand how commensal and clinical porcine enterotoxigenic E. coli strains have evolved and are engaged in the dynamic process of losing or acquiring VGs within the pig population.

Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark Wilson, Karl A Bettelheim, X Y Wu, S Driesen, James Chin, Toni Chapman, I Barchia, D Trott

Mark R Wilson

No abstract provided.

Shipborne Solar Absorption Measurements Of Co2, Ch4, N2o And Co And Comparison With Sciamachy Wfm-Doas Retrievals, T Warneke, R De Beek, M Buchwitz, J Notholt, A Schulz, Voltaire A. Velazco, O Schrems

Faculty of Science - Papers (Archive)

CO, CH4, N2O and CO2 were retrieved from high resolution solar absorption spectra obtained during a ship cruise from Capetown to Bremerhaven in January/February 2003 by Fourier Transform Infrared (FTIR) spectroscopy. Precisions of better than 0.5% for the column averaged volume mixing ratios (VMR) of CH4 and CO2 are achieved using of O2 as a reference gas. Shipborne FTIR-measurements of CO and data from SCIAMACHY/ENVISAT retrieved by the Weighting Function Modified Differential Optical Absorption Spectroscopy (WFM-DOAS) retrieval algorithm show qualitatively the same latitudinal variations. WFMDOAS data of CH4, N2O and CO2 measured over sea exhibit a great spread. The spread …

Comparing Risks Thoughtfully, Adam M. Finkel

RISK: Health, Safety & Environment (1990-2002)

Dr. Finkel argues that comparing risks is neither impossible nor immoral - but is nonetheless very difficult. He then discusses two major pitfalls of making such comparisons, one commonly cited and one routinely ignored, before sketching a framework for improving them.

Agenda: Biodiversity Protection: Implementation And Reform Of The Endangered Species Act, University Of Colorado Boulder. Natural Resources Law Center

Biodiversity Protection: Implementation and Reform of the Endangered Species Act (Summer Conference, June 9-12)

Conference organizers and/or faculty included University of Colorado School of Law professors Betsy Rieke, David H. Getches, Michael A. Gheleta and Charles F. Wilkinson.

All across the country--in Congress, in state legislatures and in urban and rural communities--people are discussing why we should or should not protect biodiversity and how best to do so. Since the Endangered Species Act is up for reauthorization, a variety of reform proposals are being debated. Speakers--including natural resource scholars, experts from the private and nonprofit sectors, and government officials--will examine the rationale for biodiversity protection, the legal framework of the Endangered Species Act, and …